How can I duplicate an object with independent meshes?
You should copy object data.
obj1 = bpy.data.objects['Cube']
data = obj1.data.copy()
obj2 = obj1.copy()
obj2.data = data
bpy.context.collection.objects.link(obj2)
obj1.location = Vector((3,0,0))
obj2.animation_data_clear()
ve = obj2.data.vertices[0]
ve.co = ve.co*2